A Mouse-Specific Model to Detect Genes under Selection in Tumors
The mouse is a widely used model organism in cancer research. However, no computational methods exist to identify cancer driver genes in mice due to a lack of labeled training data. To address this knowledge gap, we adapted the GUST (Genes Under Selection in Tumors) model, originally trained on huma...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-10-01
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| Series: | Cancers |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2072-6694/15/21/5156 |
| _version_ | 1797632143826878464 |
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| author | Hai Chen Jingmin Shu Carlo C. Maley Li Liu |
| author_facet | Hai Chen Jingmin Shu Carlo C. Maley Li Liu |
| author_sort | Hai Chen |
| collection | DOAJ |
| description | The mouse is a widely used model organism in cancer research. However, no computational methods exist to identify cancer driver genes in mice due to a lack of labeled training data. To address this knowledge gap, we adapted the GUST (Genes Under Selection in Tumors) model, originally trained on human exomes, to mouse exomes via transfer learning. The resulting tool, called GUST-mouse, can estimate long-term and short-term evolutionary selection in mouse tumors, and distinguish between oncogenes, tumor suppressor genes, and passenger genes using high-throughput sequencing data. We applied GUST-mouse to analyze 65 exomes of mouse primary breast cancer models and 17 exomes of mouse leukemia models. Comparing the predictions between cancer types and between human and mouse tumors revealed common and unique driver genes. The GUST-mouse method is available as an open-source R package on github. |
| first_indexed | 2024-03-11T11:32:44Z |
| format | Article |
| id | doaj.art-8a300bdf776843dda8aa56025c8f00e2 |
| institution | Directory Open Access Journal |
| issn | 2072-6694 |
| language | English |
| last_indexed | 2024-03-11T11:32:44Z |
| publishDate | 2023-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cancers |
| spelling | doaj.art-8a300bdf776843dda8aa56025c8f00e22023-11-10T15:00:04ZengMDPI AGCancers2072-66942023-10-011521515610.3390/cancers15215156A Mouse-Specific Model to Detect Genes under Selection in TumorsHai Chen0Jingmin Shu1Carlo C. Maley2Li Liu3College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USACollege of Health Solutions, Arizona State University, Phoenix, AZ 85004, USABiodesign Institute, Arizona State University, Tempe, AZ 85281, USACollege of Health Solutions, Arizona State University, Phoenix, AZ 85004, USAThe mouse is a widely used model organism in cancer research. However, no computational methods exist to identify cancer driver genes in mice due to a lack of labeled training data. To address this knowledge gap, we adapted the GUST (Genes Under Selection in Tumors) model, originally trained on human exomes, to mouse exomes via transfer learning. The resulting tool, called GUST-mouse, can estimate long-term and short-term evolutionary selection in mouse tumors, and distinguish between oncogenes, tumor suppressor genes, and passenger genes using high-throughput sequencing data. We applied GUST-mouse to analyze 65 exomes of mouse primary breast cancer models and 17 exomes of mouse leukemia models. Comparing the predictions between cancer types and between human and mouse tumors revealed common and unique driver genes. The GUST-mouse method is available as an open-source R package on github.https://www.mdpi.com/2072-6694/15/21/5156cancer genomicstransfer learningmolecular evolution |
| spellingShingle | Hai Chen Jingmin Shu Carlo C. Maley Li Liu A Mouse-Specific Model to Detect Genes under Selection in Tumors Cancers cancer genomics transfer learning molecular evolution |
| title | A Mouse-Specific Model to Detect Genes under Selection in Tumors |
| title_full | A Mouse-Specific Model to Detect Genes under Selection in Tumors |
| title_fullStr | A Mouse-Specific Model to Detect Genes under Selection in Tumors |
| title_full_unstemmed | A Mouse-Specific Model to Detect Genes under Selection in Tumors |
| title_short | A Mouse-Specific Model to Detect Genes under Selection in Tumors |
| title_sort | mouse specific model to detect genes under selection in tumors |
| topic | cancer genomics transfer learning molecular evolution |
| url | https://www.mdpi.com/2072-6694/15/21/5156 |
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